Sam2fastq module

This module allow to convert a SAM file into a FASTQ file.

  • Internal name: sam2fastq
  • Available: Both local and distributed mode

  • Input port:
    • input: data to convert (in SAM format)

  • Output ports:
    • fastq: converted data (in FASTQ format)


  • Mandatory parameter: None

  • Optional parameter:
    • Parameter Type Description Default value
    hadoop.reducer.task.count integer The count of Hadoop reducer tasks to use for this step. This parameter is only used in Hadoop mode Not set
  • Configuration example:
    • <!-- Convert SAM to FASTQ step -->
<step id="mysam2fastqstep" skip="false" discardoutput="false">
	<module>sam2fastq</module>
	<parameters/>
</step>